id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18746	Graphics hardware encountered an error and was reset	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-13.7.8-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
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Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/alyahussain/Desktop/aqy2_paradoxus.cxs

Log from Tue Sep 9 10:45:21 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/alyahussain/Downloads/fold_432_aqy2/fold_432_aqy2_model_0.cif

Chain information for fold_432_aqy2_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open /Users/alyahussain/Downloads/fold_15_aqy2/fold_15_aqy2_model_0.cif

Chain information for fold_15_aqy2_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show ""Color Actions""

> set bgColor white

> ui tool show Matchmaker

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_432_aqy2_model_0.cif, chain A (#1) with
fold_15_aqy2_model_0.cif, chain A (#2), sequence alignment score = 1512.5  
RMSD between 250 pruned atom pairs is 0.246 angstroms; (across all 289 pairs:
16.836)  
  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_432_aqy2_model_0.cif, chain A (#1) with
fold_15_aqy2_model_0.cif, chain A (#2), sequence alignment score = 1512.5  
RMSD between 250 pruned atom pairs is 0.246 angstroms; (across all 289 pairs:
16.836)  
  

> select #1/A

2199 atoms, 2258 bonds, 289 residues, 1 model selected  

> ui tool show ""Color Actions""

> set bgColor cadet blue

> set bgColor white

> color sel deep sky blue target ac

> color sel olive drab target ac

> select #2/A

2200 atoms, 2259 bonds, 289 residues, 1 model selected  

> color sel peru target ac

> color sel dark sea green target ac

> color sel sky blue target ac

> color sel light sky blue target ac

> color sel light green target ac

> color sel pale green target ac

> color sel dark sea green target ac

> color sel light green target ac

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> select #1/A:33

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:33

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:38

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:38

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:38

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:38

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> open /Users/alyahussain/Downloads/fold_15_aqy1/fold_15_aqy1_model_0.cif

Chain information for fold_15_aqy1_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open /Users/alyahussain/Downloads/fold_432_aqy1/fold_432_aqy1_model_0.cif

Chain information for fold_432_aqy1_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #2 models

> hide #1 models

> ui tool show Matchmaker

> matchmaker #4 to #3

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_15_aqy1_model_0.cif, chain A (#3) with
fold_432_aqy1_model_0.cif, chain A (#4), sequence alignment score = 1586.8  
RMSD between 244 pruned atom pairs is 0.326 angstroms; (across all 305 pairs:
18.225)  
  

> ui tool show ""Color Actions""

> select #3/A

2306 atoms, 2366 bonds, 305 residues, 1 model selected  

> color sel dark violet target ac

> color sel slate blue target ac

> select #4/A

2309 atoms, 2370 bonds, 305 residues, 1 model selected  

> color sel dark slate blue target ac

> color sel medium slate blue target ac

> color sel medium orchid target ac

> color sel light steel blue target ac

> color sel powder blue target ac

> color sel light sky blue target ac

> color sel teal target ac

> color sel cornflower blue target ac

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #4/A

Alignment identifier is 4/A  

> select #3/A:13

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:13

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4/A:13

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/A:13

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4/A:137

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #4/A:137

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:137

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:137

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #1 models

> show #2 models

> hide #3 models

> hide #4 models

> open /Users/alyahussain/Downloads/1J4N.cif

Summary of feedback from opening /Users/alyahussain/Downloads/1J4N.cif  
---  
note | Fetching CCD BNG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/BNG/BNG.cif  
  
1J4N.cif title:  
Crystal Structure of the AQP1 water channel [more info...]  
  
Chain information for 1J4N.cif #5  
---  
Chain | Description | UniProt  
A | AQUAPORIN 1 | AQP1_BOVIN 1-271  
  
Non-standard residues in 1J4N.cif #5  
---  
BNG — nonyl beta-D-glucopyranoside (Beta-NONYLGLUCOSIDE; nonyl beta-D-
glucoside; nonyl D-glucoside; nonyl glucoside)  
  
1J4N.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  

> open /Users/alyahussain/Downloads/1J4N-assembly2.cif

1J4N-assembly2.cif title:  
Crystal Structure of the AQP1 water channel [more info...]  
  
Chain information for 1J4N-assembly2.cif #6  
---  
Chain | Description  
A A-2 A-3 A-4 A-5 A-6 A-7 A-8 | AQUAPORIN 1  
  
Non-standard residues in 1J4N-assembly2.cif #6  
---  
BNG — nonyl beta-D-glucopyranoside (Beta-NONYLGLUCOSIDE; nonyl beta-D-
glucoside; nonyl D-glucoside; nonyl glucoside)  
  

> select
> #5/A#6/A#6//chain_id='A-2'#6//chain_id='A-3'#6//chain_id='A-4'#6//chain_id='A-5'#6//chain_id='A-6'#6//chain_id='A-7'#6//chain_id='A-8'

17022 atoms, 17136 bonds, 2475 residues, 2 models selected  

> style sel stick

Changed 17022 atom styles  

> hide sel atoms

> show sel cartoons

> hide #1 models

> hide #2 models

> hide #5 models

> hide #6 models

> show #3 models

> show #4 models

> show #6 models

> hide #3 models

> hide #4 models

> open ""/Users/alyahussain/Downloads/fold_432_aqy2/fold_432_aqy2_model_0 copy
> 3.cif""

Chain information for fold_432_aqy2_model_0 copy 3.cif #7  
---  
Chain | Description  
A | .  
  

> open ""/Users/alyahussain/Downloads/fold_432_aqy2/fold_432_aqy2_model_0 copy
> 2.cif""

Chain information for fold_432_aqy2_model_0 copy 2.cif #8  
---  
Chain | Description  
A | .  
  

> open ""/Users/alyahussain/Downloads/fold_432_aqy2/fold_432_aqy2_model_0
> copy.cif""

Chain information for fold_432_aqy2_model_0 copy.cif #9  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
[Repeated 2 time(s)]

> open ""/Users/alyahussain/Downloads/fold_15_aqy2/fold_15_aqy2_model_0 copy
> 3.cif""

Chain information for fold_15_aqy2_model_0 copy 3.cif #10  
---  
Chain | Description  
A | .  
  

> open ""/Users/alyahussain/Downloads/fold_15_aqy2/fold_15_aqy2_model_0 copy
> 2.cif""

Chain information for fold_15_aqy2_model_0 copy 2.cif #11  
---  
Chain | Description  
A | .  
  

> open ""/Users/alyahussain/Downloads/fold_15_aqy2/fold_15_aqy2_model_0
> copy.cif""

Chain information for fold_15_aqy2_model_0 copy.cif #12  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
[Repeated 2 time(s)]

> select #6//chain_id='A-8'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> hide sel target a

> hide sel cartoons

> select #6//chain_id='A-3'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> select #6//chain_id='A-8'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> select #6//chain_id='A-7'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> cartoon hide sel

> select #6//chain_id='A-6'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> cartoon hide sel

> select #6//chain_id='A-5'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> cartoon hide sel

> ui tool show Matchmaker

> select #6/A

2029 atoms, 1953 bonds, 366 residues, 1 model selected  

> matchmaker #9,12 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_432_aqy2_model_0
copy.cif, chain A (#9), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_15_aqy2_model_0
copy.cif, chain A (#12), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> select #6//chain_id='A-2'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #8,11 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-2 (#6) with fold_432_aqy2_model_0 copy
2.cif, chain A (#8), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-2 (#6) with fold_15_aqy2_model_0 copy
2.cif, chain A (#11), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> matchmaker #8,11 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-2 (#6) with fold_432_aqy2_model_0 copy
2.cif, chain A (#8), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-2 (#6) with fold_15_aqy2_model_0 copy
2.cif, chain A (#11), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> select #6//chain_id='A-3'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #7,10 to #6

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_432_aqy2_model_0 copy
3.cif, chain A (#7), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_15_aqy2_model_0 copy
3.cif, chain A (#10), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> matchmaker #7,10 to #6

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_432_aqy2_model_0 copy
3.cif, chain A (#7), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_15_aqy2_model_0 copy
3.cif, chain A (#10), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> select #6//chain_id='A-4'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #1-2 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-4 (#6) with fold_432_aqy2_model_0.cif,
chain A (#1), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-4 (#6) with fold_15_aqy2_model_0.cif,
chain A (#2), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> matchmaker #1-2 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-4 (#6) with fold_432_aqy2_model_0.cif,
chain A (#1), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-4 (#6) with fold_15_aqy2_model_0.cif,
chain A (#2), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> matchmaker #1-2 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-4 (#6) with fold_432_aqy2_model_0.cif,
chain A (#1), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-4 (#6) with fold_15_aqy2_model_0.cif,
chain A (#2), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> select #6/A

2029 atoms, 1953 bonds, 366 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #9,12 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_432_aqy2_model_0
copy.cif, chain A (#9), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_15_aqy2_model_0
copy.cif, chain A (#12), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> matchmaker #9,12 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_432_aqy2_model_0
copy.cif, chain A (#9), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A (#6) with fold_15_aqy2_model_0
copy.cif, chain A (#12), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> hide #6 models

> show #1 models

> show #2 models

> show #6 models

> select #6//chain_id='A-3'

1852 atoms, 1890 bonds, 249 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #9,12 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-3 (#6) with fold_432_aqy2_model_0
copy.cif, chain A (#9), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-3 (#6) with fold_15_aqy2_model_0
copy.cif, chain A (#12), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> matchmaker #9,12 to #6 & sel

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1J4N-assembly2.cif, chain A-3 (#6) with fold_432_aqy2_model_0
copy.cif, chain A (#9), sequence alignment score = 502.3  
RMSD between 180 pruned atom pairs is 0.825 angstroms; (across all 241 pairs:
7.298)  
  
Matchmaker 1J4N-assembly2.cif, chain A-3 (#6) with fold_15_aqy2_model_0
copy.cif, chain A (#12), sequence alignment score = 503.7  
RMSD between 180 pruned atom pairs is 0.818 angstroms; (across all 241 pairs:
7.330)  
  

> select

40472 atoms, 40381 bonds, 6216 residues, 12 models selected  

> hide sel & #1-2,6-12 atoms

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> select #10/A

2200 atoms, 2259 bonds, 289 residues, 1 model selected  

> select #12/A

2200 atoms, 2259 bonds, 289 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light gray target ac

> select #11/A

2200 atoms, 2259 bonds, 289 residues, 1 model selected  

> color sel light gray

> select #10/A

2200 atoms, 2259 bonds, 289 residues, 1 model selected  

> color sel light gray

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A #7/A #8/A #9/A

Alignment identifier is 1  

> sequence chain #2/A #10/A #11/A #12/A

Alignment identifier is 2  

> select #2/A:38 #10/A:38 #11/A:38 #12/A:38

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #2/A:38 #10/A:38 #11/A:38 #12/A:38

36 atoms, 32 bonds, 4 residues, 4 models selected  
. [ID: 2] region 4 chains [38] RMSD: 36.839  
  

> select #2/A:39-40 #10/A:39-40 #11/A:39-40 #12/A:39-40

60 atoms, 56 bonds, 8 residues, 4 models selected  

> select #2/A:35-40 #10/A:35-40 #11/A:35-40 #12/A:35-40

208 atoms, 208 bonds, 24 residues, 4 models selected  
. [ID: 2] region 4 chains [35-40] RMSD: 35.657  
  

> select #2/A:38 #10/A:38 #11/A:38 #12/A:38

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #2/A:38 #10/A:38 #11/A:38 #12/A:38

36 atoms, 32 bonds, 4 residues, 4 models selected  
. [ID: 2] region 4 chains [38] RMSD: 36.839  
  

> select #1/A:49

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:38

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:38

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> save /Users/alyahussain/Desktop/aqy2_paradoxus.cxs

——— End of log from Tue Sep 9 10:45:21 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir9,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
      OS Loader Version: 577.140.2~30

Software:

    System Software Overview:

      System Version: macOS 13.7.8 (22H730)
      Kernel Version: Darwin 22.6.0
      Time since boot: 1 hour, 22 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a51
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Graphics		duplicate						all	ChimeraX